Clunking noise on trans tail shaft

I've been trying to figure out where this noise is coming from for about 2 weeks already. Its really annoying and getting to me. I have a 2000 Gt automatic with 3200 stall and an IRS in the rear. There is a clunking noise when I drive the car in drive, 2nd gear and low 1 but does not make the noise in reverse. I thought it was the U-joints so I replaced them and nothing. But when trying to take off the drive shaft it was so tight that the yoke that goes in the tail shaft was so far in that there wasnt no play to push it in and for it to come of the rear end pinion. So I lowered the rear end and it slid out. I was looking at the transmission mount and loosened it and tryed to readjust it. But yet the mount wasnt lining up with bolts hole where it mounts to the frame/body. So I took the mount of the trans to see it the mount was bent and it wasnt. It lined up perfect where the holes should go but the 2 main screw that go to the trans wasnt lining up. The trans was still to far back. So I figured the K-member was off line. So the next day lifted the engine, loosened all the bolts to the k-memeber and lined it up. Everything was looking good so far but once I sat the engine back down the transmission bolts didnt line up any more and the driveshaft yolk was all the way in the tailshaft of the trans. So my next option was to remove the IRS and see if it was off or not. I removed it and reinstalled it and still the same problem. The noise is coming from the tail shaft where the yolk goes in. I can feel the thump from the trans tunnel inside. The exhuast is completely out of the way and nothing is in near the driveline. Anybody with any ideas on what could cause the situation?

Also the car never made this noise until I got it back from the dealership to get some new keys programmed.